Use of an user defined similarity-matrix

To compute a similarity score for protein alignments, trimAl uses the Blosum62 Similarity Matrix meanwhile for DNA or RNA alignments, trimAl uses the Identity Similarity Matrix by default. However, in any case the user can use any other matrix.

Allowed combination

It is impossible to use all the trimAl's options at the same time. The first incompatibility is between -in (designed to work with a single file) and -compareset (designed to work with a set of files). Other incompatibility is between the statistical information options and the trimming methods; in order to use combination between those methods is necessary that an output file is defined. Other compatibility is between the output and html file, they should be different in order to avoid problem in their creation. It is important that a trimming is used when one or more among the options -colnumbering, -complementary and -htmlout is used.